Heuer Bio Java Bosc2008

Biojava Project Update

Bioinformatics Open Source Conference (BOSC) 2008Toronto, CA

18 Jul 2008

● Biojava home page– http://biojava.org

● Source code and related documentation:– Version 2.1 of the GNU Lesser General Public

License (LGPL)● Wiki documentation:

– Version 1.2 of the GNU Fee Documentation License

● Hosted by Open Bioinformatics Foundation (O|B|F)– http://open-bio.org

Project history

Project history

● Alphabets and Symbols● Basic Sequence

manipulation● Translation● Proteomics● Sequence I/O● Annotations● Locations and Features● BLAST and FASTA

● Counts and Distributions● Weight Matrices and

Dynamic Programming● User Interfaces● BioSQL and Sequence

Databases● Genetic Algorithms● Protein Structure● Ontologies● Phylogenomics

Major features

Latest version

● Latest version 1.6, released Apr 2008– Phylogenomics package improved and expanded

● 2007 Google Summer of Code (GSOC'07) student Boh-Yun Lee

– PDB file parser improved– Genetic algorithm package improved– Bug fixes and documentation improvements– Requires JDK 1.5 or later– Revision control migrated from CVS to Subversion

● In any software development project there is a natural tension between revolution and evolution.

● In a Free and Open Source project:– People work on their own time.– People work on what they want.– Some people are evolutionaries, others are

revolutionaries, and some are both at different times.

– Both approaches are important and need to be cultured.

● http://incubator.apache.org/learn/rules-for-revolutionaries.html

● The Second (or third) System problem

● "It's important to remember that when you start from scratch there is absolutely no reason to believe that you are going to do a better job than you did the first time."

– http://www.joelonsoftware.com/articles/fog0000000069.html

● But we're gonna try it (again) anyway

● Biojava home page– http://biojava.org

● Biojava BOF session T.B.A.